Microbial Genetics

Bacterial genomes

Most bacteria keep their essential genes on one circular chromosome in the cytoplasm, with no nucleus ¹. The genome is compact (E. coli is about 4.6 million bp) and gene-dense, with little noncoding DNA and almost no introns. Related genes often sit together in operons: several genes transcribed from one promoter as one mRNA and switched on and off together, like the lac operon for lactose use ¹.

Many bacteria also carry plasmids - small, independently replicating circles, one to many per cell ¹. They aren’t needed for basic survival, but they often carry genes that help in a particular environment, above all antimicrobial-resistance genes ². Transposons (“jumping genes”) can move resistance genes between plasmids and the chromosome.

Horizontal gene transfer

Besides inheriting genes from a parent cell, bacteria pick up DNA from neighbors - horizontal gene transfer - which is why resistance spreads so fast ¹.

A plasmid-borne gene can jump species by conjugation, so resistance can appear in an unrelated organism without any new mutation ².

Resistance genes as targets

Once a resistance gene is a known sequence, a lab can test for it directly instead of waiting a day or two for growth in the presence of drugs ²:

Rapid panels on positive blood cultures report these within hours, letting antibiotics be adjusted early. The limits:

• Detected usually means resistant, but a gene can be present and not expressed.
• Not detected doesn’t mean susceptible: other genes or mutations can cause resistance. Phenotypic susceptibility testing still runs alongside.
• Variant genes (mecC instead of mecA) can escape an assay’s primers.

Identification targets

To identify an organism, a test needs a sequence present in every member of the group and reliable as a fingerprint - usually a slowly changing essential gene ²:

• 16S rRNA gene (bacteria): about 1,500 bp, with conserved stretches where universal primers bind and nine variable regions (V1-V9) that differ by genus and species. Sequencing it identifies organisms that won’t grow or can’t be identified by phenotype. Its resolution is limited for very close relatives (it can’t separate E. coli from Shigella).
• ITS region (fungi): the internal transcribed spacers between ribosomal RNA genes, with conserved flanks around a variable core ².

Ribosomal genes are present in every cell and often in several copies (E. coli has seven rRNA operons), and each cell holds thousands of ribosomes, so rRNA targets are both universal and abundant ³. In routine bacteriology, MALDI-TOF mass spectrometry of ribosomal proteins now does most identification; sequencing handles the hard cases.

Viral genomes change fast

Viral genomes can be DNA or RNA, single- or double-stranded, and one piece or segmented ¹ (see the genome table in Chromosome and Extrachromosomal Structure). RNA viruses copy themselves with enzymes that don’t proofread, so they mutate fast ¹. One infected person carries a swarm of related variants, a quasispecies, on which drugs and immunity select. Consequences:

DNA viruses mutate more slowly, but even CMV develops resistance mutations (in UL97 and UL54) under antiviral pressure.

How microbial targets differ

Copy number sets how much template a specimen gives; conservation decides whether one assay can catch many organisms; variability decides whether a fixed probe keeps working ².

What to take from this

Bacteria carry a compact circular chromosome with operons, plus plasmids that often hold resistance genes. Transformation, transduction, and conjugation move genes between cells and species. Resistance genes like mecA, vanA/B, and carbapenemases can be detected directly, but “not detected” doesn’t mean susceptible. 16S (bacteria) and ITS (fungi) identify organisms through conserved primer sites around variable regions. RNA viruses mutate into quasispecies, which gives genotypes, drug resistance, influenza drift and shift, and primer escape.